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ran foldx and mcsm (get) for 33k dataset

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This commit is contained in:
Tanushree Tunstall 2020-07-08 20:30:32 +01:00
parent 0e71b23759
commit 01fbc2a87b
3 changed files with 14 additions and 15 deletions
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15
foldx/runFoldx.py
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@ -37,8 +37,8 @@ arg_parser.add_argument('-i', '--input_dir', help = 'Input dir containing pdb fi
arg_parser.add_argument('-o', '--output_dir', help = 'Output dir for results. By default, it assmes homedir + drug + output', default = None) arg_parser.add_argument('-o', '--output_dir', help = 'Output dir for results. By default, it assmes homedir + drug + output', default = None)
arg_parser.add_argument('-f', '--pdb_file', help = 'PDB File to process. By default, it assmumes a file called gene_complex.pdb', default = None) arg_parser.add_argument('-f', '--pdb_file', help = 'PDB File to process. By default, it assmumes a file called <gene>_complex.pdb', default = None)
arg_parser.add_argument('-m', '--mutation_file', help = 'Mutation list. By default, assumes a file called gene_test_snps.csv exists', default = None) arg_parser.add_argument('-m', '--mutation_file', help = 'Mutation list. By default, assumes a file called <gene>_snps.csv exists', default = None)
arg_parser.add_argument('-c1', '--chain1', help = 'Chain1 ID', default = 'A') # case sensitive arg_parser.add_argument('-c1', '--chain1', help = 'Chain1 ID', default = 'A') # case sensitive
arg_parser.add_argument('-c2', '--chain2', help = 'Chain2 ID', default = 'B') # case sensitive arg_parser.add_argument('-c2', '--chain2', help = 'Chain2 ID', default = 'B') # case sensitive
@ -75,16 +75,15 @@ if not indir:
if not outdir: if not outdir:
outdir = datadir + '/' + drug + '/' + 'output' outdir = datadir + '/' + drug + '/' + 'output'
# FIXME:
process_dir = datadir + '/' + drug +'/' + 'processing'
# FIXME: this is a temporary directory and should be correctly handled # FIXME: this is a temporary directory and should be correctly handled
process_dir = datadir + '/' + drug +'/' + 'processing'
os.mkdir(process_dir) os.mkdir(process_dir)
#======= #=======
# input # input
#======= #=======
# FIXME # FIXME
if pdb_filename: if pdb_filename:
pdb_name = Path(pdb_filename).stem pdb_name = Path(pdb_filename).stem
else: else:
@ -97,8 +96,8 @@ actual_pdb_filename = Path(infile_pdb).name
if mut_filename: if mut_filename:
mutation_file = mut_filename mutation_file = mut_filename
else: else:
#mutation_file = gene.lower() + '_mcsm_snps.csv' #real mutation_file = gene.lower() + '_mcsm_snps.csv' #real
mutation_file = gene.lower() + '_test_snps.csv' #test #mutation_file = gene.lower() + '_test_snps.csv' #test
infile_muts = outdir + '/' + mutation_file infile_muts = outdir + '/' + mutation_file
@ -184,7 +183,7 @@ def loadFiles(df):
def main(): def main():
pdbname = pdb_name pdbname = pdb_name
comp = '' # for complex only comp = '' # for complex only
mut_filename = infile_muts #pnca_test_snps.csv mut_filename = infile_muts #pnca_mcsm_snps.csv
mutlist = formatMuts(mut_filename, pdbname) mutlist = formatMuts(mut_filename, pdbname)
print(mutlist) print(mutlist)

6
mcsm/mcsm_wrapper.py
View file

@ -16,7 +16,7 @@ arg_parser.add_argument('-H', '--host', help='mCSM Server', default = 'http:/
arg_parser.add_argument('-U', '--url', help='mCSM Server URL', default = 'http://biosig.unimelb.edu.au/mcsm_lig/prediction') arg_parser.add_argument('-U', '--url', help='mCSM Server URL', default = 'http://biosig.unimelb.edu.au/mcsm_lig/prediction')
arg_parser.add_argument('-c', '--chain', help='Chain ID as per PDB, Case sensitive', default = 'A') arg_parser.add_argument('-c', '--chain', help='Chain ID as per PDB, Case sensitive', default = 'A')
arg_parser.add_argument('-l','--ligand', help='Ligand ID as per PDB, Case sensitive. REQUIRED only in "submit" stage') arg_parser.add_argument('-l','--ligand', help='Ligand ID as per PDB, Case sensitive. REQUIRED only in "submit" stage')
arg_parser.add_argument('-a','--affinity', help='Affinity in nM', default = 10) arg_parser.add_argument('-a','--affinity', help='Affinity in nM', default = 0.99)
#arg_parser.add_argument('-p','--pdb_file', help = 'PDB File') #arg_parser.add_argument('-p','--pdb_file', help = 'PDB File')
arg_parser.add_argument('--datadir', help = 'Data Directory') arg_parser.add_argument('--datadir', help = 'Data Directory')
arg_parser.add_argument('--debug', action='store_true', help = 'Debug Mode') arg_parser.add_argument('--debug', action='store_true', help = 'Debug Mode')
@ -60,8 +60,8 @@ in_filename_pdb = gene.lower() + '_complex.pdb'
infile_pdb = indir + '/' + in_filename_pdb infile_pdb = indir + '/' + in_filename_pdb
#in_filename_snps = gene.lower() + '_mcsm_snps_test.csv' #(outfile2, from data_extraction.py) #in_filename_snps = gene.lower() + '_mcsm_snps_test.csv'
in_filename_snps = gene.lower() + '_mcsm_snps.csv' #(outfile2, from data_extraction.py) in_filename_snps = gene.lower() + '_mcsm_snps.csv' #(outfile_mcsm_snps, from data_extraction.py)
infile_snps = outdir + '/' + in_filename_snps infile_snps = outdir + '/' + in_filename_snps
# mcsm_results globals # mcsm_results globals

8
scripts/data_extraction.py
View file

@ -73,11 +73,11 @@ arg_parser.add_argument('-g', '--gene', help='gene name (case sensitive)', defau
args = arg_parser.parse_args() args = arg_parser.parse_args()
#======================================================================= #=======================================================================
#%% variable assignment: input and output paths & filenames #%% variable assignment: input and output paths & filenames
drug = args.drug #drug = args.drug
gene = args.gene #gene = args.gene
#drug = 'pyrazinamide' drug = 'pyrazinamide'
#gene = 'pncA' gene = 'pncA'
gene_match = gene + '_p.' gene_match = gene + '_p.'
print('mut pattern for gene', gene, ':', gene_match) print('mut pattern for gene', gene, ':', gene_match)